Figure 1
From: Full-scale network analysis reveals properties of the FV protein structure organization
From the protein structure to a residue network. (A) The FV protein has 5 domains that share a strong structural similarity to FVIII, albeit they only share \({\sim }\)40% of sequence similarity4. Using the structure 7KVE as input (ref.15), we created a residue network as an undirected unweighted graph, where the residues are the nodes, and two nodes are connected by an edge if they are in close spatial proximity in the three-dimensional space (we named it FV-RIN). (B) We calculated multiple measures of centrality to quantify the importance of each node of the FV-RIN. These measures, based on different principles of local and global connectivity, displayed a moderate Spearman correlation to each other, which led us to select only a few well-known measures for the analyses. (C) The degree is simply the number of neighbors a node has, and the betweenness counts the number of shortest-paths from every node that pass through a given node. Hence, nodes with high degree and high betweenness values are among the most central residues in the protein structure.
